[gmx-users] Umbrella Pulling

[Steven Neumann]

Dear Justin and Gmx Users,

I run a pulling of my ligand away from my protein with the same mdp file
and I obtained two different plots - Force vs time (The breaking point
occured at different times with different force). Can you please explain?
My mdp file:

title       = Umbrella pulling simulation
define      = -DPOSRES_L
; Run parameters
integrator  = md
dt          = 0.002
tinit       = 0
nsteps      = 250000    ; 0.5ns
nstcomm     = 10
; Output parameters
nstxout     = 5000      ; every 10 ps
nstvout     = 5000
nstfout     = 500
nstxtcout   = 500       ; every 1 ps
nstenergy   = 500
; Bond parameters
constraint_algorithm    = lincs
constraints             = all-bonds
continuation            = yes       ; continuing from NPT
; Single-range cutoff scheme
nstlist     = 5
ns_type     = grid
rlist       = 0.9
rcoulomb    = 0.9
rvdw        = 0.9
; PME electrostatics parameters
coulombtype     = PME
fourierspacing  = 0.12
fourier_nx      = 0
fourier_ny      = 0
fourier_nz      = 0
pme_order       = 4
ewald_rtol      = 1e-5
optimize_fft    = yes
; Temperature coupling is on
tcoupl      = V-rescale                     ; modified Berendsen thermostat
tc_grps     = Protein_LIG Water_and_ions   ; two coupling groups - more
accurate
tau_t       = 0.1   0.1                     ; time constant, in ps
ref_t       = 298   298                     ; reference temperature, one
for each group, in K
; Pressure coupling is on
Pcoupl          = Parrinello-Rahman
pcoupltype      = isotropic
tau_p           = 1.0
compressibility = 4.5e-5
ref_p           = 1.0
; Generate velocities is off
gen_vel     = no
; Periodic boundary conditions are on in all directions
pbc     = xyz
; Long-range dispersion correction
DispCorr    = EnerPres
; Pull code
pull            = umbrella
pull_geometry   = distance  ; simple distance increase
pull_dim        = N N Y
pull_start      = yes       ; define initial COM distance > 0
pull_ngroups    = 1
pull_group0     = Protein
pull_group1     = LIG182
pull_rate1      = 0.016      ; 0.008 nm per ps = 8 nm per ns
pull_k1         = 200      ; kJ mol^-1 nm^-2
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